Final answer:
During the Reformation, significant debates arose over the atonement and the presence of Christ in communion, challenging traditional views like transubstantiation with new interpretations like the Calvinist commemorative view.
Step-by-step explanation:
The major debates concerning the atonement and the presence of Christ in the elements of communion emerged prominently during the Reformation. This period saw significant theological clashes over various doctrines, including ideas like transubstantiation, where the elements of bread and wine are believed to transform into the body and blood of Christ during the Eucharist. Protestants, particularly Calvinists, challenged this view, suggesting the Eucharist was purely commemorative of the Last Supper, a perspective reflected in the Anglican Church's Elizabethan Settlement of 1559.
Both the Protestant Reformation and subsequent Counter-Reformation by the Catholic Church grappled with these issues, leading to lasting changes in Christian liturgy and practice. The discussions of these topics were deeply intertwined with the power, structure, and future direction of the Church, as well as broader societal changes.